The bailiff presents that J.M. has a lime-pit standing within the borough, to the grave hurt of the neighbours. Therefore it is ordered that from henceforth it is not allowed-to-stand (ungrammatical use of the passive of this verb, with meaning indicated by context), but that it is removed entirely—under pain of 40s (i..e., for non-removal).

Wouldn't "sto" only have a impersonal passive and thus be ungrammatical here where it's intended to have a subject? I'm not sure but wouldn't it mean something like "let there be no standing" or something similar?

(Should it be "ne" instead of "non"? I thought the former is used with the subjunctive in this context.)

But the subjunctive in those two examples is being used as part of a conditional clause. I thought that when you use a subjunctive as a third-person imperative, as the original example seems to be, you have to use "ne"? But now that I look at it again I don't even understand why quod + subjunctive is being used. That seems an awful lot like translating the English construction into Latin directly.

But this is not an indirect statement -- it seems to me they're using "quod" where "ut" would have been used, or in this case "quod ... non" instead of "ne". But I misread the Aquinas quote and later on he has "sed prohibet quod fideles non eligant voluntarie infidelium iudicium" so this does seem to be something that occurs in later Latin, but as far as I can tell it's definitely off when it comes to the classical language, no?

I never said this was a conditional clause, else I wouldn't have complained about the non. I did misread the Aquinas example as a conditional clause (although I still the think that's the case with "si arbitri sententiae non stetur"). But I wouldn't consider this an example of indirect discourse, though, but I guess that depends on how you define it.